Comments (5)
YemreGurses
commented on August 28, 2024
Created a new repository and tried to run a file streaming mapping job with simple patient-mapping and a csv file. Somehow, it doesn't run my job and gives this error. Error logs is not projected in GUI:
2023-09-04_11:12:12.931 [stream execution thread for [id = f69fed7d-4ac5-4b05-a58e-2740142e4153, runId = db574629-6b9f-4592-b430-b8f66d7fe10a]] ERROR o.a.s.s.e.s.MicroBatchExecution - Query [id = f69fed7d-4ac5-4b05-a58e-2740142e4153, runId = db574629-6b9f-4592-b430-b8f66d7fe10a] terminated with error java.lang.IllegalArgumentException: Option 'basePath' must be a directory
Repo: repo.zip
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Okanmercan99
commented on August 28, 2024
No errors were detected after thorough testing with various combinations. To pinpoint the issue, please provide specific details about the settings that produced the incorrect result. @dogukan10
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dogukan10
commented on August 28, 2024
@Okanmercan99 thanks, I'll also have a look at this issue in my spare time and let you know if I encounter any problems. Assigning the issue to me.
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dogukan10
commented on August 28, 2024
I've tested it on main branch on 13/09/2023 and here is the result table:
- toFHIR-engine / Batch job
| mappingErrorHandling | sinkSettings.errorHandling | result |
|---|---|---|
| continue | continue | OK |
| continue | halt | OK |
| halt | continue | No FhirMappingJobResult log, only 1 mapping failure error (mapping_error) log, no log for invalid row error |
| halt | halt | No FhirMappingJobResult log, only 1 mapping failure error (mapping_error) log, no log for invalid row error |
- toFHIR-engine / Streaming job
| mappingErrorHandling | sinkSettings.errorHandling | result |
|---|---|---|
| continue | continue | OK |
| continue | halt | OK |
| halt | continue | No FhirMappingJobResult log, only 1 mapping failure error (mapping_error) log, no log for invalid row error. The same error message is printed a couple of times. |
| halt | halt | No FhirMappingJobResult log, only 1 mapping failure error (mapping_error) log, no log for invalid row error. The same error message is printed a couple of times. |
@Okanmercan99 I've used the same test data which I've already shared with you. With that test data, I expect to have following FhirMappingJobResult log:
- Number of Invalid Rows: 1
- Number of Not Mapped: 1
- Number of Failed writes: 1
- Number of Written FHIR resources: 7
Of course, if we have mappingErrorHanding=halt, then no resource will be generated and the mapping job will halt. In this case, we could have another field like "Number of Not Processed" or something similar to indicate that there are some rows which are not processed because of the mapping error. WDYT @suatgonul @sinaci @YemreGurses ?
Please let me know if you can not still reproduce the cases described above, we can have a test session to discuss this.
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Okanmercan99
commented on August 28, 2024
We decided to remove this feature.
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Related Issues (20)
- Internal Server Error while fetching simple structure definition of a profile
- Bug with sliced extensions HOT 1
- Support FHIR Server as a data source
- Handle job deletion if its running HOT 1
- Implement proxy for resource validation against onfhir
- Handle large csv files for terminology-services & mapping-contexts HOT 1
- Schema error when path field contains space
- Comments and descriptions to the mappings.
- Improve README by adding all possible configuration options. HOT 1
- Problem with reading archived logs HOT 1
- FHIR R5 warnings HOT 1
- Scheduling job logs cause error HOT 1
- mvn test does not run some test cases although they are detected
- Read HL7 mssages HOT 2
- Removal or alias change of a schema from a mapping HOT 1
- Handling duplicate rows in the source data
- Enhancing schema infer error messages
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- Memory issue with local terminology service
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